For question #2: Yes, "barnyard smells" is a plural noun phrase. E.g. "A smell of coffee is a good thing early in the morning"; "The barnyard smells from next door are hard to miss".
For question #1: No, the author probably didn't want to use "as if this was not the way . . .", for that could then mean that it was an open (reasonable) possibility that winter did not usually end the way the author had just described. The author intends to mean that what was just describe is the way winter usually ends in that part of the country.
Compare the original version to a present-tense mode version:
- B version: "The accident is followed by a rush of warm weather. The length of the evenings and the heat of the balmy days seem sudden and surprising, as if this was/were not the way winter finally ended in that part of the country, almost every year."
That means that that was the way winter usually ended, "almost every year", by a rush of warm weather and lengthening of the evenings and heat of the balmy days. And so, the possible statement ("this is not the way winter finally ended in that part of the country, almost every year") in the "as if" conditional is meant to be seen as false. That is why a modal remote version, such as "as if this was not" or the irrealis "were" like in "as if this were not", would be used: to indicate that falseness.
And so, the writer would use a modal remote version -- that is, "this was" or "this were" -- to indicate that that statement is false for the #B version. (Aside: modal remoteness can be signaled by the use of the irrealis "were" or by the modal use of a past-tense verb.)
That is, if the prose had been written in present-tense mode -- which it wasn't. The original prose was written in past-tense narrative mode.
And so, since the narrative prose in your original example uses past-tense mode, then, the original version could then usually/often use a past-perfect -- e.g. "as if this had (not) been" -- to indicate that modal remoteness. But many fiction writers often use the convention of using the irrealis "were" to indicate the modal remoteness, instead of using the past-perfect "had (not) been". And so, the result is what is in your original example.
Note that the past-perfect could have been used in the original example:
- original: The accident was followed by a rush of warm weather. The length of the evenings and the heat of the balmy days seemed sudden and surprising, as if this were not [or "as if this had not been"] the way winter finally ended in that part of the country, almost every year.
In these types of situations, using the irrealis "were" (instead of the past-perfect) seems to often make the reading a bit smoother, sometimes.
Also, the use of the past-perfect (instead of the irrealis "were") can sometimes be ambiguous--as to whether it is being used for modal remoteness or backshift. The use of the irrealis "were" doesn't pose that ambiguity--because it (supposedly) can't be used for backshift.
Overall, in such contexts, the irrealis "were" or the simple past-tense is more usual than the past-perfect when used after "as if" or "as though". (For more info, there's the 2002 CGEL pages 1152-3,  and , "Irrealis 'were' and the preterite".)